Category Archives: Plant Root Soil microbiome

May 20, 2020

Posted on by

Greetings from Pittsburgh, PA!

Television and movies are a welcome distraction from the current global pandemic. For this digest, I’d like to highlight two articles. The article by Sajjad et al. investigates the possibility of resurrection of ancient microbes present in the natural frozen world and is a perfect pair for the monster-of-the-week X-Files episode “Ice.” The second highlighted article focuses on the microbiome present on two ancient Slavonic parchment codices and how this data can be used to provide additional historical context. Maybe Harrison Ford can team up with Piñar et al. to create a fourth movie in the Indiana Jones Franchise based on their work?

Happy reading, everyone!

General microbiome

Effect of a novel synbiotic on Streptococcus mutans – Bijle et al. – Nature Scientific Reports

Culturomics‐based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis – Durán‐Viseras et al. – Environmental Microbiology

Review: Ecological features of the persistence of Vibrio cholerae: retrospective analysis and actual state of the problem – Menshikova et al. – Jounral of microbiology, epidemiology, and immunobiology

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage – Reji and Francis – ISME Journal

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis – Tantivitayakul et al. – Nature Scientific Reports

Plant, root, and soil microbiome

Impacts of forest conversion to plantations on the soil carbon and nitrogen dynamics, and microbial communities – Wang et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Novel yeast taxa from the cold: description of Cryolevonia giraudoae sp. nov. and Camptobasidium gelus sp. nov. – de Garcia et al. – International Journal of Systematic and Evolutionary Microbiology

Remote sensing reveals Antarctic green snow algae as important terrestrial carbon sink – Gray et al. – Nature Communications

Review: Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? – Sajjad et al. – Science of the Total Environment

Built environment

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value – Piñar et al. – Environmental Microbiology

Bioinformatics

Preprint: Efficiently processing amplicon sequencing data for microbial ecology with dadasnake, a DADA2 implementation in Snakemake – Weißbecker et al. – bioRxiv

Techniques

Editorial: Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes – McGenity et al. – Microbial Biotechnology

Discovery of thermophilic Bacillales using reduced-representation genotyping for identification – Talamantes-Becerra et al. – BMC Microbiology

May 19, 2020

Posted on by

Good afternoon from sunny South Wales!

Today’s digest has a lot of great papers, with something for just about everyone. We’ll start off with a bang, and highlight a great paper in which Rajasekaran and collegaues challenge the current dogma that human intervertebral discs are sterile using a 16S rRNA sequencing approach.

We then have an interesting, or perhaps concerning paper looking at the prevalence of underreported parasites in laboratory zebrafish populations. A must read for anybody using zebrafish models. We also have plenty of papers concerning plant and water microbiomes, including a rather huge report on ocean systems.

Finally, with the current health climate, what better paper peruse than the contribution of Qureshi et al. who have demonstrated that gender neutral bathrooms are more rapidly colonised than single gender bathrooms. If recent anecdotal news articles are to be believed (although they seldom are) it’s usually the men letting the side down. You’ve got to wash those hands!

I hope everyone is staying safe, and enjoys today’s post!

COVID-19

Preprint: Identification of five antiviral compounds from the Pandemic Response Box targeting SARS-CoV-2 – Holwerda et al.

General microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al. – Sci Rep

Human nearly-sterile sites

Human intervertebral discs harbour a unique microbiome and dysbiosis determines health and disease – Rajasekaran et al. – European Spine Journal

Human gut microbiome

Early signs of gut microbiome aging: biomarkers of inflammation, metabolism, and macromolecular damage in young adulthood – Gaydosh et al. – The Journals of Gerontology

Animal experiments

Behavioural effects of the common brain-infecting parasite Pseudoloma neurophilia in laboratory zebrafish (Danio rerio) – Midttun et al. – Sci Rep

Lactobacillus plantarum FRT10 alleviated high-fat diet–induced obesity in mice through regulating the PPARα signal pathway and gut microbiota – Cai et al. – Applied Microbial and Cell Physiology

Animal microbiome

Factors affecting the microbiome of Ixodes scapularis and Amblyomma americanum – Brinkerhoff et al. – PLoS ONE

Preprint: Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout – Walker et al.

Whole-genome sequences of an abortive Bacillus safensis strain isolated from a mare’s uterus – Little, Hillhouse and Lawhorn – Genome Sequences

Plant, root, and soil microbiome

Preprint: A fungal member of the microbial phyllosphere antagonizes infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a putative secreted hydrolase – Eitzen et al.

Preprint: Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts – Higdon et al.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood – Gómez-Brandón et al. – Sci Rep

Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups – Pent, Bahram and Põldmaa – ISME J

Endophytic fungal community in grape is correlated to foliar age and domestication – Fan et al. – Annals of Microbiology

Water and extremophile microbiome

Microbial genomics of the global ocean system – Joye and Kostka – Coloqium Report

How do microbiota associated with an invasive seaweed vary across scales? – Bonthond et al. – Molecular Ecology

Preprint: Differences in the microbiota of native and non-indigenous gelatinous zooplankton organisms in a low saline environment – Jaspers et al.

Built environment

Gender‐neutral bathroom surfaces recolonized by microbes more quickly than single gender bathrooms – Qureshi, Kedo and Berthrong – Letters in Applied Microbiology

Food microbiology

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG) – Fang et al. – BMC Microbiology

Techniques

Preprint: Evaluation of Methods to Optimise Shotgun Metagenomic Sequencing-Based Analysis of the Microbiome of Milk – Feehily et al.

May 17, 2020

Posted on by

Hello from the Sonoran Desert! It is a sunny Sunday over Tucson, Az! I find that Sundays are the best to explore new ideas and concepts, and I especially love to take the time to read a good opinion piece or parse few review papers. In today’s digest, you’ll find a fascinating review on the Tara Ocean expedition and how it changed our understanding of marine microbial communities. If you’re more interested in the human-associated microbiome, fear not! There is also great pieces on the gut microbiota in athletes and on the interaction of oral and lung microbiome in the context of lung diseases.

If like me, you are a computational biologist thinking about microbiome data all day, you should enjoy reading today’s non microbiology pick, a great perspective paper discussing the FAIR (Findable, Accessible, Interoperable and Reusable) data principle and what are the current hurdles that limit open data reuse.

Have a great Sunday!

Pregnancy and early life

Review: The impact of maternal and early life malnutrition on health: a diet-microbe perspective – Andrew J. Forgie et al. – BMC Medicine

Multi-site human microbiome

Perspective: Microbial Diagnostics for Cancer: A Step Forward but Not Prime Time Yet –  Cynthia L. Sears et al. – Cancer Cell

Human respiratory microbiome

Review: Oral-lung microbiome interactions in lung diseases –  Manoj J. Mammen et al. – Periodontology

Human gut microbiome

Review: The athletic gut microbiota – Alex E. Mohr et al. – Journal of the International Society of Sports Nutrition

Colorectal cancer occurrence and treatment based on changes in intestinal flora – Huifang Si et al. –  Seminars in cancer Biology

Animal experiments 

Microbial communities modulating brain functioning and behaviors in zebrafish: A mechanistic approach – Larica Mohanta et al. –  Microbial Pathogenesis

Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance – Ming-Yuan Xue et al. – Microbiome

Preprint: Rumen protozoa shape microbiome composition and metabolic output of fermentation – Ronnie Solomon et al. – bioRxiv

Animal microbiome (for animals in the wild)

Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development – Zhongwei Yin et al. – Microbiology

After the bite: bacterial transmission from grey seals (Halichoerus grypus) to harbour porpoises (Phocoena phocoena) – Maarten J. Gilbert et al. – Royal Society open science

Exploration of the virome of the European brown shrimp (Crangon crangon) – Benigna Van Eynde et al. – Journal of General Virology

Plant, root, and soil microbiome

Opinion: The Role of Rhizosphere Bacteriophages in Plant Health – Akbar Adjie Pratama et al. – Trends in Microbiology

Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing –  Li Chen et al. – PeerJ

Shifts of bacterial community structure and function in long-term soybean monoculture – Fengjuan Pan et al. – Archives of Agronomy and Soil Science

Bacterial Diversity in Peat Soils of Forest Ecosystems and Oil Palm Plantation – N. A. Kusai et al. – Soil Biology

Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale – Kaoping Zhang et al. – mSystems

Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil – Lateef B. Salam et al. – Bioresources and Bioprocessing

Competition for iron drives phytopathogen control by natural rhizosphere microbiomes – Shaohua Gu et al. – Nature Microbiology

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Review: Tara Oceans: towards global ocean ecosystems biology – Shinichi Sunagawa et al. – Nature Reviews Microbiology

Review: Microbial genomics amidst the Arctic crisis – Arwyn Edwards et al. – Microbial genomics

Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes – Marlène Chiarello et al. – Proceedings of the royal society biological sciences

Bioinformatics

A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals – Hyunwook Koh et al. – Microbiome

Review: A practical guide to amplicon and metagenomic analysis of microbiome data – Yong-Xin Liu et al. – Protein Cell

TAMA: improved metagenomic sequence classification through meta-analysis – Mikang Sim et al. – BMC Bioinformatics

nf-rnaSeqMetagen: A nextflow metagenomics pipeline for identifying and characterizing microbial sequences from RNA-seq data – Phelelani T. Mpangase et al. – Medicine in Microecology

My non-microbiology pick

Perspective: FAIR Data Sharing: The Roles of Common Data Elements and Harmonization – R.D.Kush et al. – Journal of Biomedical Informatics

May 9, 2020

Posted on by

Among the highlights for today, there’s an unusual preprint on using honeybees for proxy sampling of the urban microbiome, as well as a paper on the effect of captivity on the microbiome of raptors.

In some non-microbiome related news, the summarized highlights from the 5th International One Health Congress were recently published. Some of their recommendations regarding science and public health are particularly apt considering the present pandemic, and I found it to be quite an interesting read. You can find it here:

Make science evolve into a One Health approach to improve health and security: a white paper – Osterhaus et al. – One Health Outlook

I hope you’re all doing well, wherever you are!

COVID-19

Preprint: The coding capacity of SARS-CoV-2 – Finkel et al. – bioRxiv

Pregnancy and early life

An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community – Koo et al. – Royal Society of Open Science

Animal microbiome

Preprint: Host evolutionary history and ecology shape virome composition in fishes – Geoghegan et al. – bioRxiv

The fecal microbiota of wild and captive raptors – Oliveira et al. – Animal Microbiome

Plant, root, and soil microbiome

Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? – Kaplan et al. – Evolutionary Applications

Built environment

Preprint: Holobiont urbanism: sampling urban beehives reveals cities’ metagenomes – Henaff et al. – bioRxiv

Techniques

Preprint: Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution – Matsuo et al. – bioRxiv

Quantifying technical confounders in microbiome studies – Bartolomaeus et al. – Cardiovascular Research

May 7, 2020

Posted on by

Good morning! There’s a particularly broad collection of microbiome papers to share with you today, from the bacteria that hang onto wounds after debridement to the biofilms that form in the ancient ruins of a town buried by the eruption of Mount Vesuvius. A few unusual highlights include the sexually transmitted microbiome of bedbugs and the gut microbes that colonize a sea cucumber after it grows up, remove its own digestive tract and grows a new one. Some interesting new software tools are hiding in the “Bioinformatics” section at the bottom as well.

General microbiome

Intracellular Staphylococcus aureus persisters upon antibiotic exposure, Frédéric Peyrusson et al., Nature Communications

Human respiratory microbiome

Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment, Md Zohorul Islam et al., PLOS ONE

Human skin microbiome

Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds, Samuel Verbanic et al., npj Biofilms and Microbiomes

Human gut microbiome

Systemic short chain fatty acids limit antitumor effect of CTLA-4 blockade in hosts with cancer, Clélia Coutzac et al., Nature Communications

Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity, Mathilde Payen et al., Blood Advances

Animal experiments

Preprint: Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model, Miyoshi and Lee et al., bioRxiv

Dietary Fiber Protects against Diabetic Nephropathy through Short-Chain Fatty Acid–Mediated Activation of G Protein–Coupled Receptors GPR43 and GPR109A, Yan Jun Li et al., Journal of the American Society of Nephrology

Probiotic strain Lactobacillus plantarum YYC-3 prevents colon cancer in mice by regulating the tumour microenvironment, Yuanchun Yue et al., Biomedicine & Pharmacotherapy

Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity, Sarah L. Becker et al., FEMS Microbiology Ecology

Animal microbiome

Sea cucumber intestinal regeneration reveals deterministic assembly of the gut microbiome, Brooke L. Weigel, Applied and Environmental Microbiology

Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations, Sara Bellinvia et al., Proceedings of the Royal Society B

Plant, root, and soil microbiome

Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model, John W. Schroeder et al., Nature Communications

Preprint: Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments, Julia B. Gontijo et al., bioRxiv

Preprint: Community succession of the grapevine fungal microbiome in the annual growth cycle, Liu and Howell, bioRxiv

Characterizing changes in soil microbiome abundance and diversity due to different cover crop techniques, Wang and Wu et al., PLOS ONE

Preprint: Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field, Selma Cadot et al., bioRxiv

Water and extremophile microbiome

The role of changing temperature in microbial metabolic processes during permafrost thaw, Komi S. Messan et al., PLOS ONE

Built environment

Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths, De Natale and Mele et al., PLOS ONE

Probiotics/prebiotics

Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers, Denise R. Rodrigues et al., PLOS ONE

Phages and viruses

Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants, Cristian Alejandro Suarez et al., PLOS ONE

Bioinformatics

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease, Tataru and David, PLOS Computational Biology

Sequence count data are poorly fit by the negative binomial distribution, Stijn Hawinkel et al., PLOS ONE

Preprint: sPepFinder expedites genome-wide identification of small proteins in bacteria, Li and Chao, bioRxiv

Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data, Fukunaga and Iwasaki, PLOS ONE

May 1, 2020

Posted on by

Greetings from Durham, NC!

Hope everyone is doing well and staying healthy. Today’s digest includes several host-microbiome studies, environmental microbiome studies, and an intriguing EurekAlert news article.
In this light digest of today, I wanted to highlight a cool review about correlation of the oral microbiome with children’s health and a very interesting article on cell wall architecture of the gram-positive bacteria.
COVID-19 pandemic has opened a sort of Pandora’s box filled with great science along with pseudoscience. So, the digest has these two great articles from Nature: one about chloroquine and other about the race for coronavirus vaccines.
Staying at home is difficult for everyone, here is a fun activity to do: coloring space microbes book.

Stay Safe and entertained at home!!!!

COVID-19 news articles

The race for coronavirus vaccines: a graphical guide – Callaway – Nature

Chloroquine hype is derailing the search for coronavirus treatments – Ledford – Nature

General microbiome
*The architecture of the Gram-positive bacterial cell wall– Pasquina-Lemonche et al. – Nature

Pregnancy and early life
Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery – Hernandez et al. – Scientific Reports

Metabolic Effects of Bovine Milk Oligosaccharides on Selected Commensals of the Infant Microbiome—Commensalism and Postbiotic Effects – Jakobsen et al. – Metabolites

Multi-site human microbiome
*Review: Oral microbiome: possible harbinger for children’s health – Xiao et al. – Nature International Journal of Oral Science

Animal microbiome
Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen et al. – PLOS ONE

Plant, root, and soil microbiome
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean – Han et al. – The ISME Journal

Water and extremophile microbiome
Review: Exopolysaccharides from marine bacteria: production, recovery and applications – Dave et al. – Environmental Sustainability

Stromatolitic digitate sinters form under wide‐ranging physicochemical conditions with diverse hot spring microbial communities – Sriaporn et al. – gebiology

Built environment
Comparative analysis of bacterial community and functional species in oil reservoirs with different in situ temperatures – Tian et al. – International Microbiology

Bioinformatics
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions – Medlock et al. – PLOS Computational Biology

Review: The National Microbiome Data Collaborative: enabling microbiome science – Wood-Charlson et al. – Nature Reviews Microbiology

Probiotics / prebiotics
Lactobacillus plantarum NA136 ameliorates nonalcoholic fatty liver disease by modulating gut microbiota, improving intestinal barrier integrity, and attenuating inflammation – Zhao et al. -Applied Microbiology and Biotechnology

Microbes in the news
Scientists explore links between genetics, gut microbiome and memory – DOE/PACIFIC NORTHWEST NATIONAL LABORATORY

April 26, 2020

Posted on by

Greetings from Pittsburgh, PA!

Today’s digest includes several reviews, numerous host-microbiome studies, a wide variety of environmental microbiome studies, and a new book focused on Emerging Technologies in Environmental Bioremediation.

I also wanted to highlight the virtual Fermentation Mini-Seminars offered by the Applied Ecology Department at my alma mater, NC State University. During the first seminar of the series I learned about the Wild Sourdough Project, which is a community-science/citizen-science project where participants can submit observational data about their sourdough culture. If you’re missing the lab, this might be the perfect project for you!

Virtual Events

NCSU Fermentation Mini-Seminars offered every Thursday at 4pm EST from April through August

General microbiome

Special Issue: Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals – De Vrieze et al. – Microbial Biotechnology

Review: Biofilm matrixome: Extracellular components in structured microbial communities – Karygianni et al. – Trends in Microbiology

Review: Microbial symbiosis: A network towards biomethanation – Saha et al. – Trends in Microbiology

Multi-site human microbiome

Microbiota in cerebrovascular disease: A key player and future therapeutic target – Tonomura et al. – Journal of Cerebral Blood Flow & Metabolism

Review: Role of microbiome and antibiotics in autoimmune diseases – Vangoitsenhoven and Cresci – Nutrition in Clinical Practice

Human skin microbiome

Isolation and characterization of diverse microbial representatives from the human skin microbiome – Timm et al. – BMC Microbiology

Human gut microbiome

Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder – Dan et al. – Gut Microbes

Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population – Koliada et al. – BMC Microbiology

Gut microbiome reveals specific dysbiosis in primary osteoporosis – Xu et al. – Frontiers in Cellular and Infection Microbiology

Animal experiments

The clinical drug Ebselen attenuates inflammation and promotes microbiome recovery in mice after antibiotic treatment for CDI – Garland et al. – Cell Reports Medicine

Effect of oxytetracycline treatment on the gastrointestinal microbiome of critically endangered white abalone (Haliotis sorenseni) treated for withering syndrome – Parker-Graham et al. – Aquaculture

Effects of hydrolyzed fish protein and autolyzed yeast as substitutes of fishmeal in the gilthead sea bream (Sparus aurata) diet, on fish intestinal microbiome – Rimoldi et al. – BMC Veterinary Research

Animal microbiome

(My microbiome) would walk 10,000 miles: Maintenance and turnover of microbial communities in introduced dung beetles – Parker et al. – Invertebrate Microbiology

Plant, root, and soil microbiome

Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil – Asem et al. – International Journal of Systemic and Evolutionary Microbiology

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.) – Das et al. – Scientific Reports

Peat properties, dominant vegetation type and microbial community structure in a tropical peatland – Girkin et al. – Wetlands

Integrating transcriptomics and metabolomics to studies key metabolism, pathways and candidate genes associated with drought-tolerance in Carthamus tinctorius L. under drought stress – Wei et al. – Industrial Crops and Products

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China – Yang et al. – PeerJ

Water and extremophile microbiome

Impacts of an eruption on cold-seep microbial and faunal dynamics at a mud volcano – Girard et al. – Frontiers in Marine Science

Unraveling heterogeneity of coral microbiome assemblages in tropical and subtropical corals in the South China Sea – Gong et al. – Microorganisms

Anode potential-dependent protection of electroactive biofilms against metal ion shock via regulating extracellular polymeric substances – Hou et al. – Water Research

Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin – Nigro et al. – PLOS One

Near streambed flow shapes microbial guilds within and across trophic levels in fluvial biofilms – Risse-Buhl et al. – Limnology and Oceanography

Heterotrophic sulfide-oxidizing nitrate-reducing bacteria enables the high performance of integrated autotrophic-heterotrophic denitrification (IAHD) process under high sulfide loading – Zhang et al. – Water Research

Built environment (subways, indoor surfaces)

Ecological processes affecting long-term eukaryote and prokaryote biofilm persistence in nitrogen removal from sewage – Angell et al. – Genes

Long-term microbial community dynamics in a pilot-scale gas sparged anaerobic membrane bioreactor treating municipal wastewater under seasonal variations – Kannan et al. – Bioresource Technology

Book: Emerging Technologies in Environmental Bioremediation – Edited by Shah et al.

Food microbiology

How processing methods affect the microbial community composition in a cereal-based fermented beverage – Phiri et al. – LWT – Food Science and Technology

High-throughput sequencing and metabolomics reveal differences in bacterial diversity and metabolites between red and white sufu – Tang et al. – Frontiers in Microbiology

April 24, 2020

Posted on by

Events

Virtual Podium 2020 – Session 5 (Microbiome) – April 24, 2020

Scientific career and work-life balance – April 24, 2020

World Malaria Day – April 25, 2020 – Draws attention to the impact of the disease and (re)urges us to find a way to overcome it once and for all.
Join the #talkingmalaria tweetchat on April 24, 2020 at 12 noon BST.

COVID-19

GRAND CHALLENGE: A billion molecules against COVID-19 – Joint European Disruptive Initiative

General microbiome

Reversibility of propionic acid inhibition to anaerobic digestion: Inhibition kinetics and microbial mechanism – Youl Han – Chemosphere

Responses of microbial structures, functions, metabolic pathways and community interactions to different C/N ratios in aerobic nitrification – Hongwei Sun – Bioresource Technology

PERSPECTIVE: Cultivating fungal research – Heidi H. Kong – Science

Human microbiome

REVIEW: Microbiota–immune interactions in asthma pathogenesis and phenotype – Nicholas W.Lukacs – Current Opinion in Immunology

CANCER IN TRANSLATION: Microbiome genomics for cancer prediction – Lorenz Adlung – Nature Cancer

Human skin microbiome

BOOK CHAPTER: The wound microbiome – Aayushi Uberoi – In: Wound Healing, Tissue Repair, and Regeneration in Diabetes.

Human gut microbiome

BOOK CHAPTER: Dietary Fiber and Gut Microbiota – Carolina Senés-Guerrero – In: Science and Technology of Fibers in Food Systems

Animal experiments

Effect of in feed administration of different butyrate formulations on Salmonella Enteritidis colonization and cecal microbiota in broilers – Lonneke Onrust – Veterinary Research

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics – Ori Furman – Nature Communications

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer – Farnaz Fouladi – ISME Journal

Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in the cattle rumen – Javad Gharechahi – FEMS Microbiology Ecology

Animal microbiome

Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species – Guoliang Li – ISME Journal

Plant, root, and soil microbiome

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions – Stien Beirinckx – Microbiome

Regulatory relationship between quality variation and environment of Cistanche deserticola in three ecotypes based on soil microbiome analysis – Xiao Sun – Scientific Reports

Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems – Sreejata Bandopadhyay – PeerJ

Water microbiome

Total Microbial Activity and Sulfur Cycling Microbe Changes in Response to the Development of Hypoxia in a Shallow Estuary – Yunjung Park – Ocean Science Journal

Built environment

Associations Between Respiratory Infections and Bacterial Microbiome in Student Dormitories in Northern China – Xi Fu – Indoor Air

Bacterial community analysis of floor dust and HEPA filters in air purifiers used in office rooms in ILAS, Beijing – Jianguo Guo – Scientific Reports

Microbes in space

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation – Camilla Urbaniak – Microbiome

Food microbiology

Insights into the Microbiological Safety of Wooden Cutting Boards Used for Meat Processing in Hong Kong’s Wet Markets: A Focus on Food-Contact Surfaces, Cross-Contamination and the Efficacy of Traditional Hygiene Practices – Patrick T. Sekoai – Microorganisms

Pre-print

MicrobioLink: An integrated computational pipeline to infer functional effects of microbiome-host interactions – Tahila Andrighetti – bioRxiv

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi – bioRxiv

Mendelian randomization analysis revealed causal effects from gut microbiota to abdominal obesity – Qian Xu – bioRxiv

A quantitative measure of functional redundancy in microbial ecosystems – Taylor M Royalty – bioRxiv

Host association induces genome changes in Candida albicans which alters its virulence – Amanda C Smith – bioRxiv

Shirin’s non-microbiology picks

CAREER FEATURE: Safely conducting essential research in the face of COVID-19 – Virginia Gewin – Nature

Reaching a Large Urban Undergraduate Population through Microbial Ecology Course-Based Research Experiences – Samantha Parks – Journal of Microbiology & Biology Education

POLICY FORUM: Against pandemic research exceptionalism – Alex John London – Science

WORLD VIEW: On the 50th Earth Day, take collective action for the planet – Emma Marris – Nature

BEHIND THE PAPER: Annotating the unknown: Functional Gene Annotation using Untargeted Metabolomics – Robert Jansen – Nature Microbiology Community

April 23, 2020

Posted on by

The wave of new microbe enthausiasts keeps coming and with it a light digest for today.  I am writing to you from Bremen, Germany, with a selection including a wheat fungi that changes the wheat leaf microbiome and antimicrobial resistance genes identified by whole metagenome shotgun study of nasopharyngal colonization in South Africa.

There is also an interesting article about species identification errors occurring in context of large sequence collection platforms.
And to mix things up a little bit, at the end of a list you find a paper with amazing microscopy featuring the beautiful parasite Trypanosoma brucei and answering the endless question to how this parasite colonizes its insect host, the tsetse fly.

Human respiratory microbiome

Longitudinal changes in the nasopharyngeal resistome of South African infants using shotgun metagenomic sequencing – Rendani I. Manenzhe – PLOS ONE

Human gut microbiome

Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner – PLOS BIOLOGY

Animal experiments

Preprint: Comparative analysis of beneficial effects of Vancomycin treatment on Th1- and Th2-biased mice and role of gut microbiota – Pratikshya Ray – bioRxiv

Assessment of dietary supplementation with galactomannan oligosaccharides and phytogenics on gut microbiota of European sea bass (Dicentrarchus Labrax) fed low fishmeal and fish oil based diet – Simona Rimoldi – PLOS ONE

Lactobacillus reuteri attenuated allergic inflammation induced by HDM in the mouse and modulated gut microbes – Lingzhi Li – PLOS ONE

Animal microbiome

Occurrence of Mycoplasma gallisepticum in wild birds: A systematic review and meta-analysis – Anna Sawicka – PLOS ONE

Plant, root, and soil microbiome

A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition – Heike Seybold – Nature Communications

Phages and viruses

SMOOT libraries and phage-induced directed evolution of Cas9 to engineer reduced off-target activity – Derek Cerchione – PLOS ONE

Bioinformatics

BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries? – Mikko Pentisaari – PLOS ONE

Science, publishing, and career

A pedagogical approach to science outreach – Marni B. McClure – PLOS BIOLOGY

Judith’s non-microbiology picks

Trypanosoma brucei colonizes the tsetse gut via an immature peritrophic matrix in the proventriculus – Clair Rose – Nature Microbiology

April 22, 2020

Posted on by

Welcome to another post from a new volunteer! I’m a Ph.D student studying the infant gut microbiome and I’m excited to be volunteering with Microbiome Digest.

There are several preprints today, including another great study from the CHILD cohort. This one is on maternal consumption of artificially sweetened beverages and the infant gut microbiota. There is also a preprint calling for improvement in scientific conferences. Both are highlighted in green.

Pregnancy and early life

Preprint: Consumption of artificially sweetened beverages during pregnancy impacts infant gut microbiota and body mass index – Isabelle Laforest-Lapointe — bioRxiv

Oral microbiome

Preprint: Genotypic and phenotypic characterization of Streptococcus mutans isolated from dental caries – Mohammad Shahnoor Hossain – bioRxiv

Pyruvate secretion by oral streptococci modulates hydrogen peroxide dependent antagonism – Sylvio Redanz – ISME Journal

Synergism between Corynebacterium and Streptococcus sanguinis reveals new interactions between oral commensals – Puthayalai Treerat – ISME Journal

Animal experiments

The gut microbiota response to helminth infection depends on host sex and genotype – Fei Ling – ISME Journal

Animal microbiome

Lipids and small metabolites provisioned by ambrosia fungi to symbiotic beetles are phylogeny-dependent, not convergent – Yin-Tse Huang – ISME Journal

Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP) – Kshitij Tandon – ISME Journal

Plant, root, and soil microbiome

Active sulfur cycling in the terrestrial deep subsurface – Emma Bell – ISME Journal

Preprint: An antagonistic driver of the microbial phyllosphere suppresses infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a secreted hydrolase – Katharina Eitzen – bioRxiv

Preprint: Grapevine pruning time affects natural wound colonization by wood-invading fungi – Maria del Pilar Martinez-Diz – bioRxiv

Water and extremophile microbiome

Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus – M.C. Muñoz-Marín – ISME Journal

Food microbiology

Preprint: Antibiotic-resistant Salmonella species and Escherichia coli in broiler chickens from farms, abattoirs and open markets in selected districts of Zambia – Nelson Phiri – bioRxiv

Microbes in the news

Breastfeeding may lead to fewer human viruses in infants
https://www.sciencedaily.com/releases/2020/04/200415110452.htm

Science, publishing, and career

Preprint: Evaluating features of scientific conferences: A call for improvements – Sarvenaz Sarabipour – bioRxiv